9rme | pdb_00009rme
Hybrid NMR/Xray structure of SARS-CoV2 macrodomain (nsp3b) in complex with the sulfamoyl derivative of GS-441524
Structural highlights
FunctionR1A_SARS2 Multifunctional protein involved in the transcription and replication of viral RNAs. Contains the proteinases responsible for the cleavages of the polyprotein.[UniProtKB:P0C6X7] Inhibits host translation by interacting with the 40S ribosomal subunit. The nsp1-40S ribosome complex further induces an endonucleolytic cleavage near the 5'UTR of host mRNAs, targeting them for degradation. Viral mRNAs are not susceptible to nsp1-mediated endonucleolytic RNA cleavage thanks to the presence of a 5'-end leader sequence and are therefore protected from degradation. By suppressing host gene expression, nsp1 facilitates efficient viral gene expression in infected cells and evasion from host immune response.[UniProtKB:P0C6X7] May play a role in the modulation of host cell survival signaling pathway by interacting with host PHB and PHB2. Indeed, these two proteins play a role in maintaining the functional integrity of the mitochondria and protecting cells from various stresses.[UniProtKB:P0C6X7] Responsible for the cleavages located at the N-terminus of the replicase polyprotein. In addition, PL-PRO possesses a deubiquitinating/deISGylating activity and processes both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains from cellular substrates. Participates together with nsp4 in the assembly of virally-induced cytoplasmic double-membrane vesicles necessary for viral replication. Antagonizes innate immune induction of type I interferon by blocking the phosphorylation, dimerization and subsequent nuclear translocation of host IRF3. Prevents also host NF-kappa-B signaling.[UniProtKB:P0C6X7] Participates in the assembly of virally-induced cytoplasmic double-membrane vesicles necessary for viral replication.[UniProtKB:P0C6X7] Cleaves the C-terminus of replicase polyprotein at 11 sites. Recognizes substrates containing the core sequence [ILMVF]-Q-|-[SGACN]. Also able to bind an ADP-ribose-1-phosphate (ADRP).[UniProtKB:P0C6X7] Plays a role in the initial induction of autophagosomes from host reticulum endoplasmic. Later, limits the expansion of these phagosomes that are no longer able to deliver viral components to lysosomes.[UniProtKB:P0C6X7] Forms a hexadecamer with nsp8 (8 subunits of each) that may participate in viral replication by acting as a primase. Alternatively, may synthesize substantially longer products than oligonucleotide primers.[UniProtKB:P0C6X7] Forms a hexadecamer with nsp7 (8 subunits of each) that may participate in viral replication by acting as a primase. Alternatively, may synthesize substantially longer products than oligonucleotide primers.[UniProtKB:P0C6X7] May participate in viral replication by acting as a ssRNA-binding protein.[UniProtKB:P0C6X7] Plays a pivotal role in viral transcription by stimulating both nsp14 3'-5' exoribonuclease and nsp16 2'-O-methyltransferase activities. Therefore plays an essential role in viral mRNAs cap methylation.[UniProtKB:P0C6X7] Publication Abstract from PubMedViral macrodomains, which hydrolyze mono-ADP-ribosylated proteins to evade host immunity, represent emerging antiviral targets, yet their druggability remains underexplored. GS-441524, the active metabolite of remdesivir, has been identified as an inhibitor of the SARS-CoV-2 (severe acute respiratory syndrome coronavirus) macrodomain (Nsp3b). Herein, the structure-activity relationship governing macrodomain recognition by the ribosylated moiety using a panel of nucleoside analogs, revealing that phosphate configuration and nucleobase identity critically modulate binding affinity. GS-441524 derivatives exhibit up to 200-fold higher affinity compared to adenosine-based ligands. A novel sulfamoyl derivative demonstrates superior inhibitory potency, attributable to its occupation of the phosphate subsite and formation of a stabilizing hydrogen-bond network. These findings provide molecular insights into Nsp3b-ligand interactions and establish a rational framework for the development of high-affinity, structure-guided inhibitors targeting viral macrodomains. Structure-Based Rational Design of a Selective Hydrolase Inhibitor of the Severe Acute Respiratory Syndrome Coronavirus-2 Nsp3 Macrodomain.,Krishnathas R, Mineev KS, Fourkiotis NK, Touret F, Sideras-Bisdekis C, Tsika AC, Gande SL, Linhard V, Sreeramulu S, Lennartz F, Weiss MS, Coutard B, Spyroulias GA, Schwalbe H Chembiochem. 2025 Nov 27;26(23):e202500593. doi: 10.1002/cbic.202500593. Epub , 2025 Nov 2. PMID:41176653[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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